7G9Z

PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1216822028

PDB DOI: https://doi.org/10.2210/pdb7G9Z/pdb
Deposition Group: G_1002270 (changed state) ExploreG_1002270

Classification: VIRAL PROTEIN
Organism(s): Zika virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-03 Released: 2023-07-26
Deposition Author(s): Godoy, A.S., Noske, G.D., Fairhead, M., Lithgo, R.M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Marples, P.G., Ni, X., Tomlinson, C.W.E., Wild, C., Mesquita, N.C.M.R., Oliva, G., Fearon, D., Walsh, M.A., von Delft, F.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.212
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

PanDDA analysis group deposition

Godoy, A.S., Noske, G.D., Fairhead, M., Lithgo, R.M., Koekemoer, L., Aschenbrenner, J.C., Balcomb, B.H., Marples, P.G., Ni, X., Tomlinson, C.W.E., Wild, C., Mesquita, N.C.M.R., Oliva, G., Fearon, D., Walsh, M.A., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 49.56 kDa
Atom Count: 3,946
Modelled Residue Count: 435
Deposited Residue Count: 435
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	A	435	Zika virus	Mutation(s): 0 EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1 Go to UniProtKB: Q32ZE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q32ZE1
Sequence AnnotationsExpand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZVB (Subject of Investigation/LOI) Query on ZVB Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-(propan-2-yl)-1H-pyrrolo[3,2-b]pyridine C₁₀ H₁₂ N₂ OKEHFANNANVSEO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.212
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.709	α = 90
b = 69.498	β = 92.38
c = 57.473	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19AI171399
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/07600-3

Revision History (Full details and data files)

Version 1.0: 2023-07-26
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

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